A church-controlled organization is a branch of a church, including a men's or women's group, a religious school, a mission society, or a youth group. If you are establishing a Church as an entity, note that in the application under specific products/services.
A Church (NOT Church Controlled Organization):
For tax purposes, a "church" refers to any organization claiming to be a church or any convention or association of churches. The word "church" includes temples, mosques, and other houses of worship. To be considered a church for tax purposes, a group must be part of an organized religion, must have a mission statement, and must be formally organized as a distinct legal entity.